Faculty Opinions recommendation of Mapping and analysis of chromatin state dynamics in nine human cell types.

By I. K. Jordan, Ahsan Huda. 2011

441 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/d439c2957da7c66d2bc653edb3a71c0635675da5

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Citations in the corpus

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs (2014, methodology): “…ISMARA’s results on ChIP-seq data, we make use of data from the ENCODE Project in which, besides gene expression, nine different chromatin marks were measured across eight different cell types (all modifications and cell types are listed in Supplemental Tables 4 and 5) (Ernst et al. 2011).”
Modification of enhancer chromatin: what, how and why? (2013, background): “These interactions can be affected by charge-nullifying modifications such as lysine acetylation, particularly occurring in the context of histone globular domains (Fenley et al., 2010).”
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression (2012, background): “This view has been altered, however, as a plethora of novel RNA species has been discovered (see, for instance, Carninci et al. 2005; Denoeud et al. 2007; Kapranov et al. 2007; Findeiss et al. 2010).”
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs (2012, background): “We have further investigated the exonic behavior of a number of chromatin modifications (Ernst et al. 2011, monitored through ChIP-seq in K562, see Supplemental Information and Methods) depending on the exon coSI value in chromatin-associated RNA.”
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012, background): “These endeavors typically use sophisticated machine learningmethods (Ernst and Kellis 2010; Ernst et al. 2011; A Mortazavi, S Pepke, G Marinov, and B Wold, in prep.) with complex and varying sensitivity to ChIP strength; and such efforts can be very sensitive to data quality.”